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python-package.yml
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name: Python package
on:
push:
branches: [ "main", "master" ]
pull_request:
branches: [ "main", "master" ]
jobs:
build:
runs-on: ${{ matrix.os-version }}
name: ${{ matrix.os-version }} (${{ matrix.python-version }})
strategy:
fail-fast: false
matrix:
os-version: ["ubuntu-latest"]
python-version: ["3.9"] # ["3.8", "3.9", "3.10"]
steps:
- uses: actions/checkout@v3
- name: "Set up Python ${{ matrix.python-version }}"
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
cache: 'pip'
- name: "Install flake8"
run: |
pip install flake8
- name: "Lint with flake8"
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: "Install miniconda"
uses: conda-incubator/setup-miniconda@v2
with:
miniconda-version: "latest"
auto-update-conda: true
mamba-version: "*"
python-version: ${{ matrix.python-version }}
channels: conda-forge,bioconda
environment-file: environment.yml
- name: "Install pytest"
shell: bash -l {0}
run: |
python -m pip install --upgrade pip
pip install setuptools wheel build pytest
- name: "Test with pytest"
shell: bash -l {0}
run: |
pytest -s